Revisiting molecular descriptors with TDiMS for interpretable intramolecular interactions based on substructure pairs

Abstract

Molecular descriptors play a crucial role in representing the structural features of molecules for machine learning-based physical property prediction. However, current descriptors either consider only local aspects of molecular structures or fail to effectively learn nonlocal structural features involving long-distance intramolecular interactions. Here, to address this issue, we present a descriptor named TDiMS. TDiMS effectively summarizes the enumerated pairwise topological distances between molecular substructures, thus capturing nonlocal interactions. Our evaluation shows that TDiMS successfully identifies essential features of large structures and outperforms other representative descriptors in predicting properties for which distances between substructures are a primary factor. In addition, these identified features are highly interpretable for experts in materials discovery. A descriptor, TDiMS, is developed to summarize the enumerated pairwise topological distances between molecular substructures and identify interpretable molecular features for materials discovery.